Search Results for "molecular dynamics simulation" - Page 3
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Showing 74 open source projects for "molecular dynamics simulation"
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QDC (quick direct-method controlled) is an optimized exact implementation of the Gillespie's direct-method. It is designed for biochemical simulations when there is the need of dynamic parameters whose values can change during the simulation.
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SMMP (Simple Molecular Mechanics for Proteins) is a program library for protein simulations with an emphasis on advanced Monte Carlo algorithms. It includes various force fields to calculate the energy of a protein and protein-protein interactions.
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PyBact is an open source software written in Python for Bacterial Identification. The software generates simulated data matrix which accurately represents the probabilistic positive/negative results of the tested biochemical test.
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Combines Blender's graphical interface and rendering capabilities with MBDyn's multi-body dynamics, aerodynamics, and aeroelastics simulation and analysis, for rapid modeling and realistic rendering of physics based multi-body simulations.
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MIPGen
Simple Molecular Interaction Potential Generator in Python
Molecular Interaction Potential Generator MIPGEN is a python program that will calculate Molecular Interaction Potential grids over a given molecule, that could be either a protein or a small organic compound (drug). The output will be a series of grids with DX format (*.dx) that the user will be able to visualize using any Molecular visualization program like VMD, PyMol, Chimera... For more information on dependencies and usage, please read the Documentation. Users are welcome... -
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FAUNUS is an object oriented class library for molecular simulation, written in C++. It contains routines and utility programs for, Metropolis Monte Carlo sampling (NVT, NPT, NmuT ensembles), Macromolecules, Proton Titration, Widom Analysis etc.
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pyFoam is a Python front-end to the OpenFOAM (Open Source CFD Toolbox). It introduces interactivity into OpenFOAM, simplifies connection with third-party functionality and streamlines design of custom user solvers
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"JSBSim Python Bindings" is a Python wrapper around the open source flight dynamics model JSBSim (http://jsbsim.sourceforge.net/). It allows to use most of the JSBSim C++ API from the Python programming language.
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Translates OpenFOAM (Open Source CFD Toolbox, see http://sourceforge.net/projects/foam) data into MED format (see http://www.code-aster.org/outils/med). The initial goal to develop this utility was to be able integrate OpenFOAM functionality with SALOME
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Guanxi is a robust analysis and simulation application for Social Network Analysts. Guanxi allows researchers in the field to create, import, and export an endless array of networks, analyze their structure, and run custom dynamics over them.
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Use SASSIE to generate and manipulate large numbers of molecular structures and then calculate the SAXS, SANS, and neutron reflectivity profiles from atomistic structures. Use for intrinsically disordered proteins. We need alpha-testers and developers.
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PyMani is a program for robotic manipulator simulation. Designed for testing manipulator dynamics and as an educational tool for teaching the robotic parameters. This project currently uses Python, VPython, SymPy, PyODE, and wxPython.
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Spasmos is a Python package that allows scientists to simulate the dynamics of highly collisional plasmas using a number of numerical methods.
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MBDyn_sim_suite is a collection of free pre&post-processing tools and simulation models for the open-source multi-body analysis software MBDyn forming a general purpose simulation environment for structural dynamics with an emphasis on wind turbines.
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This is the first force-matching software published with the ability to do general coarse-graining for molecular systems.
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BrennerMD is a public domain Fortran molecular dynamics program by Donald Brenner and other people. This project is to maintain the original source code and to build a Python interface on top of it.
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This project is A Mitochondrial OxydoReduction Simulation System. It consists of two linked projects: a program for displaying and analysing large biomolecular systems (Floral) and a multi-agent simulator for biomolecular oxydoreduction systems (AMORSS).
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Esra is a 100% pure java library for the interactive analysis of molecular mechanics data. Mangles your data in your favorite scripting language.
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Cellogica is a cellular logic analysis tool. It incorporates sequential logic and finite state machine to elucidate the relationship between transcription factors and corresponding gene expression.
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ĄHola!, for "Hordes of Little Atoms," is a project to develop a lean, modular, scalable toolkit for massive simulations of particle (molecular) dynamics. It is written in C and Python to get the best balance between programmer and run time.
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Software package for stochastic and hybrid simulation of microtubule dynamics and the effects of anti-mitotic drugs and microtubule regulatory proteins.
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PyAero
CFD Toolkit
PyAero is a toolkit developped at andheo for CFD software : post-processing, curve generation, … Currently PyAero focuses on ONERA's code "Cedre". PyAero is powered by Qt, Python, PySide, enthought and pyLot. -
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CarDriver is an educational Virtual Environment for safer driving. It is a game written in Python and Panda3D where you are the driver of a car and have to care about the traffic rules. It uses the Open Dynamics Engine (ODE) for the physical simulation.
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openSim is a software platform for the creation, simulation and visualization of system dynamics models.
